Here's a place where I can post my thoughts on new papers, provide updates on my projects, and post info that will eventually be on my website The Theropod Database - http://theropoddatabase.com/ . It will center on theropods, but may delve into other topics as well such as phylogenetics.

Friday, July 12, 2019

Phylogeny of the Lori analysis 2 - Topology

Now that we've covered my philosophy in designing the Lori analysis, let's look at some of the basic relationships it recovered. The details are all laid out in the paper of course, and I'll write a post on each main clade as part of this series.

Something I'd like to clarify is that some commentary I've read has been to the effect of 'the support for lots of these clades is low, so be skeptical.' That's true in the broad sense, but my point was that TWiG analyses over the past two decades also have low support for these clades, they just hardly ever report it. You see e.g. Deinonychosauria again and again not because it's strongly supported in any TWiG analysis, but rather because scorings are reused and each analysis weakly supports Deinonychosauria based on the same weak character evidence. So don't think the Lori analysis has unusually weak support for these clades, but rather that previous TWiG analyses don't report their support levels so you never knew how weak they were.

In any case, here's the full topology of taxa I consider strongly supported as maniraptoromorphs...

Prior to Maniraptoriformes, we have a series of compsognathid-grade taxa including compsognathids themselves. One surprise was finding Haplocheirus in Compsognathidae instead of Alvarezsauroidea. As far as I know, this has only been previously suggested by Alifanov and Saveliev (2011:184) without proposed evidence, and based only on the initial description. I used Choiniere's (2010) detailed thesis description to score the taxon, so incomplete scoring isn't an issue here. I thought adding the new Xiyunykus and Bannykus might pull it toward alvarezsaurs, but nope, although scoring them in more detail after further description might influence things. "Eight characters used by Choiniere et al. (2010) to place it in the latter clade were not included, but it also requires nine steps to constrain there in our analysis ... This suggests neither a compsognathid nor an alvarezsauroid identification is well supported and more study is needed."

The next 'big picture' concept is a fairly standard maniraptoriform topology of ornithomimosaurs branching first, then alvarezsaurs and therizinosaurs, then Pennaraptora. What I found interesting about this area of the tree is that it's highly unstable. As I wrote, "only four steps are required
to get a result similar to Sereno’s (1999) where alvarezsauroids are sister to ornithomimosaurs
and therizinosaurs sister to that pair. Similarly, while we recover a pairing of alvarezsauroids
and therizinosaurs to the exclusion of pennaraptorans, placing therizinosaurs closer
to the latter clade merely needs three additional steps. Positioning alvarezsauroids sister
to Pennaraptora or putting therizinosaurs just outside Maniraptoriformes are slightly
less parsimonious at six steps each..." So Maniraptora is not the stable clade, Pennaraptora is. For instance, moving therizinosaurs sister to oviraptorosaurs as used to be common in the late 90s-early 00s requires 13 steps while placing alvarezsaurs as paravians takes 11 steps.

Alternative topologies for major maniraptoriform clades in the Lori matrix showing the number of extra steps needed from the most parsimonious trees.

Similarly, there are a few taxa in this non-pennaraptoran maniraptoriform grade which have 'consensus positions' that are actually very poorly supported. Pelecanimimus and Nqwebasaurus are ornithomimosaurs, right? Well, Nqwebasaurus seems more likely to be an alvarezsaur as it "requires six steps to be an ornithomimosaur ... [and] all but two characters recovered by Choiniere et al. (2012) as supporting an ornithomimosaurian placement were included." Pelecanimimus is more ambiguous, although it's most parsimoniously an alvarezsaur in my trees. "Constraining it as an ornithomimosaur only requires two additional steps, however, where it emerges just above Shenzhousaurus as in Macdonald and Currie (2018). As only two of their characters supporting an ornithomimosaurian identification were not used by us, and only one from Brusatte et al. (2014), its true position is unclear pending a detailed osteology such as Perez-Moreno’s (2004) unreleased description." The third controversial taxon of this kind is Fukuivenator, "emerging as the first branching alvarezsauroid, but moving to a basal therizinosauroid position with only two steps. A more stemward position seems more likely than a relationship with dromaeosaurids as suggested in its original description or Cau (2018), as it can be a coelurid with only four more steps, but takes seven steps to be sister to Pennaraptora and 11 steps to be paravian." I'd now add Lingyuansaurus to this list, though it was published after submission time. Recall it it a supposed therizinosaur, but moves to Ornithomimosauria with just three more steps.

Whatever Hesperornithoides is, it's clearly paravian, and paravian topology proved particularly labile in my analysis. Your initial reaction might be 'hey, Xu et al. 2011 were right, and Archaeopteryx is a basal deinonychosaur." Maybe. But placing archaeopterygids (including 'anchiornithines') as avialans or sister to troodontids is only a step longer each. Add to this scansoriopterygids, which are avialans in the most parsimonious trees but move to basal paravians in a single step, and troodontids, which are deinonychosaurs but move to Avialae in a single step, and the basic topology of Paraves is uncertain. This isn't to say all alternatives are great though, as dromaeosaurids closer to birds than troodontids takes six more steps, and archaeopterygids basal to troodontids, dromaeosaurids and avialans takes 15 more steps. Oviraptorosaurian scansoriopterygids are 12 steps longer. So we have a subset of plausible alternatives, and that's where the research should be focusing. Stratigraphically basal deinonychosaurian archaeopterygids and basal avialan scansoriopterygids make sense, but who knows.

Alternative topologies for major paravian clades in the Lori
matrix showing the number of extra steps needed from the most
parsimonious trees.

The fifth major paravian clade is Unenlagiidae, traditionally paired with dromaeosaurids but here uniquely recovered as sister to Dromaeosauridae plus Troodontidae. This Unenlagiidae includes halszkaraptorines as in Senter et al. (2012) and Cau (2018). One interesting point is that the position of unenlagiids varies with the position of archaeopterygids- when archaeopterygids are sister to troodontids in trees one step longer, unenlagiids are sister to dromaeosaurids. But when archaeopterygids are avialans in trees one step longer, so are unenlagiids as in Agnolin and Novas (2013). Besides the standard set of taxa, we recovered the Gondwanan Pyroraptor and Ornithodesmus as unenlagiines as well as Dakotaraptor. If the latter is true, is that a situation like Titanis and Alamosaurus where a southern taxon moved into North America? New halszkaraptorines include the Early Cretaceous Ningyuansaurus and ISMD-VP09.

Finally, let's go over the basal avialan results. I've always recovered Balaur as an avialan as in Cau et al. (2015) and it takes 8 steps to move to Dromaeosauridae. Surprisingly, Hesperonychus groups with Balaur instead of microraptorians. It only takes three steps to move to Microraptoria, but the stratigraphy is a better fit by Balaur. "The branching order of Jehol non-ornithothoracine birds has been contentious, with our matrix supporting Sapeornis branching first, followed by jeholornithids then confuciusornithiforms. Jeholornithids branching first is only three steps longer, but Sapeornis branching last as in some recent analyses requires 12 more steps." Between confuciusornithiforms and Ornithothoraces are Chongmingia, Yandangornis and Jinguofortis. "... Jinguofortis joins Chongmingia in only three steps. Our analysis supports the latter’s position close to Ornithothoraces as in p2 of Wang et al.’s (2016) figure 7, whereas moving it to their p1 more stemward of Jeholornis and Sapeornis requires 11 more steps."

There are hundreds of other things to say about the topology, but next time I'm going to switch gears and discuss my first successful experience with peer review. In the mean time, if any of you have questions about taxon placements or alternative topologies, feel free to ask.

Choiniere, 2010. Anatomy and systematics of coelurosaurian theropods from the
Late Jurassic of Xinjiang, China, with comments on forelimb evolution in Theropoda.
PhD thesis, George Washington University. 994 pp.

Choiniere, Forster and De Klerk, 2012. New information on Nqwebasaurus thwazi,
a coelurosaurian theropod from the Early Cretaceous Kirkwood Formation in South Africa.
Journal of African Earth Sciences. 71-72, 1-17. DOI: 10.1016/j.jafrearsci.2012.05.005

Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria:
Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail.
PLOS ONE. 7(5), e36790. DOI: 10.1371/journal.pone.0036790.

Macdonald and Currie, 2018. Description of a partial Dromiceiomimus (Dinosauria: Theropoda)
skeleton with comments on the validity of the genus. Canadian Journal of Earth Sciences. 56(2), 129-157. DOI: 10.1139/cjes-2018-0162

Hartman, Mortimer, Wahl, Lomax, Lippincott and Lovelace, 2019. A new
paravian dinosaur from the Late Jurassic of North America supports a
late acquisition of avian flight. PeerJ7:e7247. DOI: 10.7717/peerj.7247

35 comments:

How stable is the grouping of Archaeopteryx with other archaeopterygids? This group has been alternatively known as Anchiornithidae so it's rather important to know how solidly Archaeopterygidae being the right name for it is.

Sofar as Unenlagiidae goes, do you think it would be a good idea to redefine it to be excluded from Dromaeosauridae even in the traditional placement where it's considered a subfamily? Given this let's us always use the family name instead of switching all the time. Likewise, Unenlagiinae could become the name for the traditional grouping within the family, since Halszkaraptorinae is also included.

It depends on your starting tree and what topology you're constraining. If Archaeopteryx is a deinonychosaur, forcing it to be basal to anchiornithines plus other deinonychosaurs takes 12 extra steps. If Archaeopteryx is an avialan, forcing it closer to Aves than anchiornithines takes 5 steps. I've recently scored each Archaeopteryx specimen seperately (except the Maxburg and chicken wing) and am in the process of scoring 8 Anchiornis specimens separately, so we'll have better data on this soon.

Correlated shifting of clades is also frequent in my analysis. Usually, some clades have a couple of favorite alternative placements, and move to one of these alternatives according to other clade movements. Usually, one options are: branches forming a paraphyletic grade A + others forming clade B, vs clade A + grade B.

Note that all unenlagiines have been found in deposits younger than the Cenomanian, and we'll have to wait for a newly described raptor dino from South America to confirm that Unenlagiinae and Halszkaraptorinae form a distinct clade to the exclusion of troodontids and all dromaeosaurids traditionally assigned to Microraptoria, Dromaeosaurinae, and Velociraptorinae.

Ornithodesmus is Barremian, if my assignment is correct. Also, the Solnhofen Alcmonavis emerged there when I added it after submission. So we might get some earlier members, and both European interestingly enough.

Assuming that your initial placement of Ornithodesmus in Unenlagiinae is correct, then Ornithodesmidae would have priority over Unenlagiinae and Unenlagiidae, and Unenlagiinae could become a subfamily given Ornithodesmus' older age.

"Assuming that your initial placement of Ornithodesmus in Unenlagiinae is correct, then Ornithodesmidae would have priority over Unenlagiinae and Unenlagiidae, and Unenlagiinae could become a subfamily given Ornithodesmus' older age."

Technically yes, but realistically Ornithodesmus is only weakly supported as going there, so I wouldn't recommend changing any family-level names until better evidence than the Lori analysis was presented.

"That would make six origins of flight, two of them within Unenlagiidae/Ornithodesmidae!"

Unless Alcmonavis was closer to Rahonavis than to flightless unenlagiines, or if unenlagiines were primitively volant and lost flight 1-4 times.

Ornithodesmus is among several taxa that had multiple equally parsimonious positions, so we pruned it a posteriori from the published cladogram. I list all of these taxa and their recovered range of positions in the supplementary info under "Positions of maniraptoromorphs pruned a posteriori." In the case of Ornithodesmus, it's an "Unenlagiine in the Pyroraptor+Unenlagia clade."

I would love some comment on the additional lengths to recover more traditional arrangements for eudromaeosaurs. Dromaeosaurus nested within asian "velociraptorine" taxa rather than Utahraptor and co. is one of the more bizarre placements in your tree for mine.

An interesting thing about the dromaeosaurid part of the tree is that most suggested basic rearrangements happen in two steps or less. I found that Dromaeosaurinae is more inclusive than usual, and that Deinonychus and the Utah+Achillo pair make a third main clade. Rearranging these three clades into any combination takes 2 steps. Forcing Dromaeosaurus closer to Utah+Achillo than Deinonychus also takes 2 steps (IGM 100/22+23 follows).

Some questions about more basal Coelurosauria, i.e. those more basal than the Ornitholestes+ clade shown in the cladogram.1) "several taxa usually considered members of [Compsognathidae] (e.g., Huaxiagnathus, Juravenator, Mirischia, Sinocalliopteryx) branch off more basally"I don't see Mirischia on the cladogram. Is that because it is more basal than Ornitholestes, or because it is difficult to pin down?

2) "Megaraptorans and a clade of proceratosaurids and coelurids branch first after tyrannosauroids"Which was more basal?

3) "megaraptorans or the coelurid-proceratosaurid group can be constrained to Tyrannosauroidea in only four steps"Is it that both groups simultaneously go to Tyrannosauroidea in only four steps? Or each group separately? If separately, how many steps for both megaraptorans and coelurids+proceratosaurids to end up in Tyrannosauroidea?

4) Is the Proceratosauridae you recovered limited to the usual suspects (Proceratosaurus, Guanlong, Sinotyrannus, Kileskus), or does it include others (e.g. Juratyrant, Stokesosaurus), as in Loewen et al. (2013)?

5) Where did you find Bicentenaria, Zuolong, and Chilesaurus?

Lastly, The cladogram only shows Ornitholestes+, but your analysis was much larger. Did you exclude the rest just for the sake of space? or because you're worried readers won't heed your warning that the matrix is not well-suited for assessing the relationships of non-Maniraptoromorphs?

First, the mpt is in the tnt file, so anyone can view it. I'll post about it here at some point.

"I don't see Mirischia on the cladogram. Is that because it is more basal than Ornitholestes, or because it is difficult to pin down?"

It's a proceratosaurid/coelurid.

""Megaraptorans and a clade of proceratosaurids and coelurids branch first after tyrannosauroids"Which was more basal?"

Megaraptorans.

"Is it that both groups simultaneously go to Tyrannosauroidea in only four steps? Or each group separately? If separately, how many steps for both megaraptorans and coelurids+proceratosaurids to end up in Tyrannosauroidea?"

Separately in 4 steps each. Have yet to check if both are forced there at once.

"Is the Proceratosauridae you recovered limited to the usual suspects (Proceratosaurus, Guanlong, Sinotyrannus, Kileskus), or does it include others (e.g. Juratyrant, Stokesosaurus), as in Loewen et al. (2013)?"

Proceratosaurids and coelurids mix together. Sinotyrannus is sister to Yutyrannus in Tyrannosauroidea, while Juratyrant is sister to Eotyrannus in Tyrannosauroidea. Stokesosaurus was excluded as it was too unstable.

"5) Where did you find Bicentenaria, Zuolong, and Chilesaurus?"

In the saved tree, Bicentenaria is a eustreptospondylid megalosauroid and Zuolong is the most basal megaraptoran. I can't remember if they can fall out in other places though. Chilesaurus was not included since I have no confidence its an averostran, but came out as an alvarezsauroid in an earlier version. I still have it scored, so I could check.

"The cladogram only shows Ornitholestes+, but your analysis was much larger. Did you exclude the rest just for the sake of space? or because you're worried readers won't heed your warning that the matrix is not well-suited for assessing the relationships of non-Maniraptoromorphs?"

Closer to the latter. They were included to help attract potential coelurosaur mimics like Afromimus and to provide a decently extensive outgroup to polarize Coelurus', Tanycdolagreus' and Ornitholestes' character states, to help test Rauhut's idea Lori could be a juvenile of those. But the topology itself is not based on good assumptions, so it's not something I wanted confused for a useful result.

I would need to score Protoavis. Which sounds like a fun project and post, but merely out of historical interest since David's correct that the Protoavis animal hypothesized by Chatterjee isn't a thing.

The paper "Pre-Archaeopteryx coelurosaurian dinosaurs and their implications for understanding avian origins". Archaeopterygids are deinonychosaurs, scansoriopterygids are oviraptorosaurs & the latter are sister to birds.

Apologies for indulging a personal tic and beating a dead language to death, as I know your specialty is phylogeny and not alpha taxonomy or Clessical languages, but the statement, from the *Hesperornithoides* description, that "[t]he trivial epithet honors the Miessler family" is not quite accurate.

That may have been the intent, but in actuality the form *miessleri* can only honor a single male individual of that family.

I've seen it argued that since "the Miessler family" is a singular unit, the "-i" suffix is technically acceptable. Much like how, say, Vegavis iaai uses the "-i" suffix, even though "the Instituto Antártico Argentino (IAA) expedition that collected the specimen" was made up of multiple people. Whereas had the etymology been "for Howard and Helen Miessler," the "-orum" suffix would be mandatory. At least, that's what Peter Dodson claimed in defense of the original spelling of Avaceratops lammersi, in his book The Horned Dinosaurs. The current ceratopsid literature does call it "lammersi."

Off a skim of the paper and post it's never addressed how solid the grouping of Unenlagiinae and Halskaraptorinae is - how easy is it to move Halskaraptorinae to any number of other positions in Deinonychosauria?

I'm not sure how much stock I should put in the topology of crown Aves, given that it wasn't the focus of the paper. But are you surprised that "saltariensis" (I guess this is "Martinavis saltariensis") and _Limenavis_ both end up among the palaeognaths?